This script uses the data.frame “data”, loaded from s01.RData. That is, all rows with C==“C” has been excluded for exploratory data analysis.

# ------------------------------------------------------------------
#  Prepare environment
# ------------------------------------------------------------------
# load packages
source(file = file.path("Scripts","Setup","setup01_projectPackages.R")) 
# load output from s01_DatasetPrep.R
load(file=file.path("Scripts","s01.RData"))

# White background in plots
theme_set(theme_bw()) # to be replaced with a azTheme
update_geom_defaults("point", list(shape = 1))

Are the plots and tables also being written to file?

## [1] TRUE

1 Baseline covariates

1.1 Numeric summaries

1.1.1 Entire dataset

The markdown/latex notation for tables does not work for html output. Notified the authour of pixidust.

Table 6: Continuous covariates
Characteristic mean (SD) [range] Missing (N (%))
Age (yrs) 39.000 (8.590), [17.000-60.0] 0 (0.00)
Serum creatinine (mg/dL) 0.835 (0.166), [0.459-1.3] 4 (6.67)
eGFR (mL/min/1.73m^2^) 99.400 (32.200), [46.500-212.0] 4 (6.67)
Body weight (kg) 75.200 (11.400), [56.000-102.0] 2 (3.33)
Body height (cm) 176.000 (11.100), [152.000-208.0] 2 (3.33)
Body mass index (kg/m^2^) 24.300 (3.900), [17.100-35.2] 4 (6.67)


Table 7: Categorical covariates
Characteristic Category N (%)
Sex Female 26 (43.30)
Male 34 (56.70)
Race White 19 (31.70)
Black/African American 9 (15.00)
Asian 14 (23.30)
Other 18 (30.00)
Ethnicity Hispanic/Latino 11 (18.30)
Not Hispanic/Latino 17 (28.30)
Not Reported 16 (26.70)
Unknown 16 (26.70)
Renal impairment Normal 33 (55.00)
Mild 20 (33.30)
Moderate 3 (5.00)
Missing 4 (6.67)


1.1.2 Stratified by study

Table 8: Continuous covariates by study
Study Characteristic mean (SD) [range] Missing (N (%))
d0000c0001 Age (yrs) 41.100 (7.800), [27.000-60.00] 0 (0.00)
Serum creatinine (mg/dL) 0.796 (0.129), [0.484-1.08] 2 (6.67)
eGFR (mL/min/1.73m^2^) 106.000 (29.300), [63.900-198.00] 2 (6.67)
Body weight (kg) 76.600 (11.100), [56.000-102.00] 1 (3.33)
Body height (cm) 180.000 (11.800), [159.000-208.00] 2 (6.67)
BMI (kg/m^2^) 23.700 (3.570), [17.200-29.80] 3 (10.00)
d0000c0002 Age (yrs) 36.800 (8.930), [17.000-51.00] 0 (0.00)
Serum creatinine (mg/dL) 0.874 (0.191), [0.459-1.30] 2 (6.67)
eGFR (mL/min/1.73m^2^) 92.700 (34.100), [46.500-212.00] 2 (6.67)
Body weight (kg) 73.900 (11.800), [57.000-99.00] 1 (3.33)
Body height (cm) 172.000 (9.160), [152.000-198.00] 0 (0.00)
BMI (kg/m^2^) 24.800 (4.170), [17.100-35.20] 1 (3.33)


Table 9: Categorical covariates by study
Study Characteristic Category N (%)
d0000c0001 Sex Female 8 (26.70)
Male 22 (73.30)
Race White 11 (36.70)
Black/African American 3 (10.00)
Asian 8 (26.70)
Other 8 (26.70)
Ethnicity Hispanic/Latino 7 (23.30)
Not Hispanic/Latino 8 (26.70)
Not Reported 7 (23.30)
Unknown 8 (26.70)
Renal impairment Normal 19 (63.30)
Mild 9 (30.00)
Missing 2 (6.67)
d0000c0002 Sex Female 18 (60.00)
Male 12 (40.00)
Race White 8 (26.70)
Black/African American 6 (20.00)
Asian 6 (20.00)
Other 10 (33.30)
Ethnicity Hispanic/Latino 4 (13.30)
Not Hispanic/Latino 9 (30.00)
Not Reported 9 (30.00)
Unknown 8 (26.70)
Renal impairment Normal 14 (46.70)
Mild 11 (36.70)
Moderate 3 (10.00)
Missing 2 (6.67)


1.1.3 Stratified by dose

Table 10: Continuous covariates by dose
Dose Characteristic mean (SD) [range] Missing (N (%))
25 Age (yrs) 39.700 (8.200), [28.000-51.000] 0 (0.00)
Serum creatinine (mg/dL) 0.895 (0.237), [0.459-1.300] 1 (6.67)
eGFR (mL/min/1.73m^2^) 90.900 (41.500), [46.500-212.000] 1 (6.67)
Body weight (kg) 74.700 (10.400), [59.000-97.000] 0 (0.00)
Body height (cm) 171.000 (6.280), [160.000-181.000] 0 (0.00)
BMI (kg/m^2^) 25.500 (3.720), [21.300-35.200] 0 (0.00)
100 Age (yrs) 40.900 (7.530), [28.000-51.000] 0 (0.00)
Serum creatinine (mg/dL) 0.800 (0.150), [0.484-1.080] 1 (6.67)
eGFR (mL/min/1.73m^2^) 108.000 (35.200), [63.900-198.000] 1 (6.67)
Body weight (kg) 80.200 (12.900), [56.000-102.000] 1 (6.67)
Body height (cm) 179.000 (10.300), [159.000-196.000] 1 (6.67)
BMI (kg/m^2^) 24.700 (3.370), [20.400-29.800] 2 (13.30)
150 Age (yrs) 41.300 (8.320), [27.000-60.000] 0 (0.00)
Serum creatinine (mg/dL) 0.792 (0.108), [0.659-0.989] 1 (6.67)
eGFR (mL/min/1.73m^2^) 104.000 (23.200), [64.700-137.000] 1 (6.67)
Body weight (kg) 73.200 (8.090), [60.000-87.000] 0 (0.00)
Body height (cm) 181.000 (13.400), [166.000-208.000] 1 (6.67)
BMI (kg/m^2^) 22.800 (3.620), [17.200-29.100] 1 (6.67)
300 Age (yrs) 33.900 (8.910), [17.000-50.000] 0 (0.00)
Serum creatinine (mg/dL) 0.854 (0.138), [0.542-1.120] 1 (6.67)
eGFR (mL/min/1.73m^2^) 94.400 (26.100), [64.200-176.000] 1 (6.67)
Body weight (kg) 73.000 (13.500), [57.000-99.000] 1 (6.67)
Body height (cm) 173.000 (11.500), [152.000-198.000] 0 (0.00)
BMI (kg/m^2^) 24.000 (4.630), [17.100-32.900] 1 (6.67)


Table 11: Categorical covariates by dose
Dose Characteristic Category N (%)
25 Sex Female 8 (53.30)
Male 7 (46.70)
Race White 5 (33.30)
Black/African American 2 (13.30)
Asian 3 (20.00)
Other 5 (33.30)
Ethnicity Hispanic/Latino 2 (13.30)
Not Hispanic/Latino 4 (26.70)
Not Reported 5 (33.30)
Unknown 4 (26.70)
Renal impairment Normal 7 (46.70)
Mild 4 (26.70)
Moderate 3 (20.00)
Missing 1 (6.67)
100 Sex Female 4 (26.70)
Male 11 (73.30)
Race White 5 (33.30)
Black/African American 3 (20.00)
Asian 4 (26.70)
Other 3 (20.00)
Ethnicity Hispanic/Latino 6 (40.00)
Not Hispanic/Latino 2 (13.30)
Not Reported 2 (13.30)
Unknown 5 (33.30)
Renal impairment Normal 9 (60.00)
Mild 5 (33.30)
Missing 1 (6.67)
150 Sex Female 4 (26.70)
Male 11 (73.30)
Race White 6 (40.00)
Asian 4 (26.70)
Other 5 (33.30)
Ethnicity Hispanic/Latino 1 (6.67)
Not Hispanic/Latino 6 (40.00)
Not Reported 5 (33.30)
Unknown 3 (20.00)
Renal impairment Normal 10 (66.70)
Mild 4 (26.70)
Missing 1 (6.67)
300 Sex Female 10 (66.70)
Male 5 (33.30)
Race White 3 (20.00)
Black/African American 4 (26.70)
Asian 3 (20.00)
Other 5 (33.30)
Ethnicity Hispanic/Latino 2 (13.30)
Not Hispanic/Latino 5 (33.30)
Not Reported 4 (26.70)
Unknown 4 (26.70)
Renal impairment Normal 7 (46.70)
Mild 7 (46.70)
Missing 1 (6.67)


2 Plots of distributions and correlations

2.1 Entire dataset

2.1.1 Continuous

The diagonal graphs show histograms of each covariate. The lower off-diagonal graphs are scatter plots of observations (black open circles) with linear regression (black line) and its 95% confidence interval (grey shaded area). The lower off-diagonal graphs show the Pearson’s correlation coefficient. The graphs are displayed in red if the Pearson’s correlation coefficient is > 0.4.

2.1.2 Categorical

The diagonal graphs show bar charts of each covariate. The off-diagonal graphs show the correlation between covariate categories: the black point is a visual reference point, and the numbers are percentage of subjects of a covariate split by the groups of the other covariate. For example, the bottom left graph show that within the group with normal renal function, 19% are female and 81% are male (numbers aligned left of the reference point). Similarly, within the group of females, 29% have normal, 36% have mild, 21% have moderate renal impairment and 14% is missing information (numbers aligned above the reference point). NA refers to not available, i.e., missing. 

## Warning in dev(file = filename, width = dim[1], height = dim[2], ...):
## failed to load cairo DLL

2.1.3 Categorical versus continuous

The black line within the box shows the median and the box’s upper and lower edges show the inter quartile range (IQR). Whiskers extend to the highest value that is within 1.5*IQR. Data beyond the end of the whiskers are outliers and plotted as points. NA refers to not available, i.e., missing.

2.2 Distributions stratified by study

2.3 Distributions by dose group/regimen

The black line within the box shows the median and the box’s upper and lower edges show the inter quartile range (IQR). Whiskers extend to the highest value that is within 1.5*IQR. Data beyond the end of the whiskers are outliers and plotted as points.

The diagonal graphs show bar charts of each covariate. The off-diagonal graphs show the correlation between covariate categories: the black point is a visual reference point, and the numbers are percentage of subjects of a variable split by the groups of the other variable. NA refers to not available, i.e., missing. See also example text for categorical covariate correlation above.

3 Time-varying covariates versus time

3.1 Stratified by study

3.1.1 Continuous

The lines connect data from one individual. Ticks indicate all individual records of the covariate in the dataset. The blue line with shaded area is a loess smooth and its 95% confidence interval indicating any overall trends in changes of covariate values over time after first dose.

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3.1.2 Categorical

The lines are a step function connecting data from one individual. Ticks indicate all individual records of the covariate in the dataset.

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3.2 Stratified by subject

3.2.1 Continuous

Ticks indicate all individual records of the covariate in the dataset.

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3.3 Categorical

The lines are a step function connecting data from one individual. Ticks indicate all individual records of the covariate in the dataset.

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